Locus 1017

Sequence ID 2L_DroMel_CAF1
Location 2,903,286 – 2,903,465
Length 179
Max. P 0.905688
window1630 window1631 window1632

overview

Window 0

Location 2,903,286 – 2,903,405
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 86.14
Mean single sequence MFE -20.46
Consensus MFE -14.10
Energy contribution -13.22
Covariance contribution -0.88
Combinations/Pair 1.23
Mean z-score -2.10
Structure conservation index 0.69
SVM decision value 0.47
SVM RNA-class probability 0.748772
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2903286 119 + 22407834
UUUGGACAUCUCCAUCCUAUUACUAUGAUAUUGAAACAAUGUAUAUGAUGUGCUUUAUUUAUUUAAUAUUUGAAGCAUUCCAUUGCACAUUCCCAUCCCUAAUCUGUGCAUUCCAUUGC
..((((....))))......................(((((...(((..((((((((..(((...)))..))))))))..)))((((((...............))))))...))))). ( -21.46)
>DroSec_CAF1 21907 119 + 1
UUCGGAAAUUACCAUCCUAUUACUAUGAUAUUGAAACAAUGCAUGUGAUGUGCUUUAUUUAUUUAAUAUCUGAAGCAUUCUAUUGCACAUUCCCAUCCCUAAUCUGUGCAUUCCACUGC
...((((...........(((((.(((.(((((...)))))))))))))((((((((..(((...)))..)))))))).....((((((...............))))))))))..... ( -22.16)
>DroSim_CAF1 22318 119 + 1
UUCGGAAAUUACCAUCCUAUUACUAUGAUAUUGAAACAAUGUAUGUGAUGUGCUUUAUUUAUUUAAUAUUUGAAGCAUUCUAUUGCACAUUCCCAUCCCUAAUCUGUGCAUUCCACUGC
...((((...........(((((....((((((...))))))..)))))((((((((..(((...)))..)))))))).....((((((...............))))))))))..... ( -22.26)
>DroEre_CAF1 22520 112 + 1
UUCGCA--UGAGCACUCUCCUAC-----AAUUGAAACAAUGUAUAUGAUGUGCUUUAUUUAUUUAAUAUUUGAAGCGUUCUAUUGCACAUUCCCAUCUCUAAUCUGUGCAUUCCACUGC
...(((--.((((((((...(((-----(.(((...)))))))...)).))((((((..(((...)))..))))))))))...((((((...............))))))......))) ( -18.66)
>DroYak_CAF1 22658 112 + 1
UUCGCA--UGAGUUUUUUCCUAC-----UCUUAAAACAAUGUAUAUGAUGUGCUUUAUUUAUUUAAUUUUCGAAGCAUUCCAUUGCACAUUUCCAUCUCUAAUCUGUGCAUUCCACUGC
...(((--(((((........))-----)).......(((((..(((..(((((((...............)))))))..)))...)))))..............)))).......... ( -17.76)
>consensus
UUCGGA_AUGACCAUCCUAUUACUAUGAUAUUGAAACAAUGUAUAUGAUGUGCUUUAUUUAUUUAAUAUUUGAAGCAUUCUAUUGCACAUUCCCAUCCCUAAUCUGUGCAUUCCACUGC
...((......))...............................(((..((((((((..(((...)))..))))))))..)))((((((...............))))))......... (-14.10 = -13.22 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,903,366 – 2,903,465
Length 99
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 78.06
Mean single sequence MFE -29.25
Consensus MFE -15.34
Energy contribution -15.98
Covariance contribution 0.64
Combinations/Pair 1.06
Mean z-score -2.18
Structure conservation index 0.52
SVM decision value 1.04
SVM RNA-class probability 0.905688
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2903366 99 + 22407834
CAUUGCACAUUCCCAUCCCUAAUCUGUGCAUUCCAUUGCCACUUUUUGUGU--GUC-GCUU-------------CCCGAAAGGAUUCUUU-UGGGGCAUGGAGCAUGGAGC---UAGCU
..................(((.(((((((..(((((.(((((.....))).--...-....-------------((((((((....))))-))))))))))))))))))..---))).. ( -28.40)
>DroSec_CAF1 21987 94 + 1
UAUUGCACAUUCCCAUCCCUAAUCUGUGCAUUCCACUGCCACUUUUUGUGU--GUC-GCUC-------------CCCAAAAGGAUUCUUU-UUGG-----GGGCAUGGAUC---UAGCA
...((((((...............)))))).((((..(((((.....))).--)).-((.(-------------(((((((((...))))-))))-----)))).))))..---..... ( -28.46)
>DroSim_CAF1 22398 95 + 1
UAUUGCACAUUCCCAUCCCUAAUCUGUGCAUUCCACUGCCACUUUUUGUGU--GUC-GCUC-------------CCCGAAAGGAUUCUUUUUUGG-----GGGCAUGGAGC---UAGCU
...((((((...............))))))(((((..(((((.....))).--)).-((.(-------------(((((((((....))))))))-----)))).))))).---..... ( -27.76)
>DroEre_CAF1 22593 109 + 1
UAUUGCACAUUCCCAUCUCUAAUCUGUGCAUUCCACUGCCACUUUUUGUGU--GUGUGCCCCAUUGCCAGUCGGUUCGAAAGGAUUCUUU-U--G-----GGGCAUGGUGCAUGGUGCA
...(((((.................(((((((.....(((((.....))).--))((((((((.....((...((((....)))).))..-)--)-----))))))))))))).))))) ( -31.07)
>DroYak_CAF1 22731 104 + 1
CAUUGCACAUUUCCAUCUCUAAUCUGUGCAUUCCACUGCCACUUUUUGUGUGUGUGUGCCCCAUUGCCAGUCGGUCCGAAAGGAUUCUUU-U--G-----GGGCAUGU-------UGCA
...((((((...............))))))...(((.(((((.....))).)))))(((((((.....((...((((....)))).))..-)--)-----)))))...-------.... ( -30.56)
>consensus
UAUUGCACAUUCCCAUCCCUAAUCUGUGCAUUCCACUGCCACUUUUUGUGU__GUC_GCUC_____________CCCGAAAGGAUUCUUU_U_GG_____GGGCAUGGAGC___UAGCA
...((((((...............)))))).((((.((((((.....))..........................((....))..................)))))))).......... (-15.34 = -15.98 +   0.64)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,903,366 – 2,903,465
Length 99
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 78.06
Mean single sequence MFE -28.06
Consensus MFE -14.88
Energy contribution -15.32
Covariance contribution 0.44
Combinations/Pair 1.05
Mean z-score -1.84
Structure conservation index 0.53
SVM decision value 0.16
SVM RNA-class probability 0.612592
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2903366 99 - 22407834
AGCUA---GCUCCAUGCUCCAUGCCCCA-AAAGAAUCCUUUCGGG-------------AAGC-GAC--ACACAAAAAGUGGCAAUGGAAUGCACAGAUUAGGGAUGGGAAUGUGCAAUG
.....---..(((((((....((((((.-((((....)))).)))-------------..))-)..--.(((.....))))).))))).((((((..(((....)))...))))))... ( -25.50)
>DroSec_CAF1 21987 94 - 1
UGCUA---GAUCCAUGCCC-----CCAA-AAAGAAUCCUUUUGGG-------------GAGC-GAC--ACACAAAAAGUGGCAGUGGAAUGCACAGAUUAGGGAUGGGAAUGUGCAAUA
.....---..(((((((((-----((((-((.......)))))))-------------).))-...--.(((.....)))...))))).((((((..(((....)))...))))))... ( -29.60)
>DroSim_CAF1 22398 95 - 1
AGCUA---GCUCCAUGCCC-----CCAAAAAAGAAUCCUUUCGGG-------------GAGC-GAC--ACACAAAAAGUGGCAGUGGAAUGCACAGAUUAGGGAUGGGAAUGUGCAAUA
.....---..(((((((((-----((...((((....)))).)))-------------).))-...--.(((.....)))...))))).((((((..(((....)))...))))))... ( -26.40)
>DroEre_CAF1 22593 109 - 1
UGCACCAUGCACCAUGCCC-----C--A-AAAGAAUCCUUUCGAACCGACUGGCAAUGGGGCACAC--ACACAAAAAGUGGCAGUGGAAUGCACAGAUUAGAGAUGGGAAUGUGCAAUA
....((((((....(((((-----(--(-...(((....)))...((....))...)))))))...--.(((.....)))))).)))..((((((..(((....)))...))))))... ( -31.10)
>DroYak_CAF1 22731 104 - 1
UGCA-------ACAUGCCC-----C--A-AAAGAAUCCUUUCGGACCGACUGGCAAUGGGGCACACACACACAAAAAGUGGCAGUGGAAUGCACAGAUUAGAGAUGGAAAUGUGCAAUG
....-------...(((((-----(--(-......(((....)))((....))...)))))))(((...(((.....)))...)))...((((((..((.......))..))))))... ( -27.70)
>consensus
UGCUA___GCUCCAUGCCC_____CC_A_AAAGAAUCCUUUCGGG_____________GAGC_GAC__ACACAAAAAGUGGCAGUGGAAUGCACAGAUUAGGGAUGGGAAUGUGCAAUA
..........(((((((...............(((....)))...........................(((.....)))))).)))).((((((..(((....)))...))))))... (-14.88 = -15.32 +   0.44)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:09 2006